# HG changeset patch # User iuc # Date 1520407578 18000 # Node ID b10b77f55859ad0862e93b6ad82b2dad69be8214 # Parent 485ccb7874ad495572bfa39dde22a3316a1e4883 planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 683d64a78adb3ff671f750d969d9daee5108169d diff -r 485ccb7874ad -r b10b77f55859 hicCorrelate.xml --- a/hicCorrelate.xml Tue Jan 02 09:48:16 2018 -0500 +++ b/hicCorrelate.xml Wed Mar 07 02:26:18 2018 -0500 @@ -18,15 +18,15 @@ #end if $log1p - #if $use_range.select_use_range == "yes_use_range": - --range $range_min:$range_max - #end if + @USE_RANGE@ #if $chromosomes: --chromosomes #echo "' '".join([ "'%s'" % $chrom.chromosome for $chrom in $chromosomes ])# #end if - - --colorMap $colormap + + #if $colormap: + --colorMap $colormap + #end if --outFileNameHeatmap ./heatmap.png --outFileNameScatter ./scatter.png @@ -41,25 +41,15 @@ - - - - - - - - - - - + + + - - @@ -90,7 +80,7 @@ - + @@ -116,7 +106,7 @@ - log scale for the values - Correlate full matrix or only specific chromosomes - Correlate only within a given range. -- colormap to use: Colormap_ +- colormap to use: Colormap_ Output ------ diff -r 485ccb7874ad -r b10b77f55859 involucro Binary file involucro has changed diff -r 485ccb7874ad -r b10b77f55859 macros.xml --- a/macros.xml Tue Jan 02 09:48:16 2018 -0500 +++ b/macros.xml Wed Mar 07 02:26:18 2018 -0500 @@ -1,6 +1,13 @@ \${GALAXY_SLOTS:-4} - 2.0 + 2.1 + + + #if $use_range.select_use_range == "yes_use_range": + --range $range_min:$range_max + #end if + + hicexplorer @@ -19,6 +26,23 @@ + + + + + + + + + + + + + + + + + @@ -300,13 +324,12 @@ - - + - + @@ -556,9 +579,9 @@ + label="Include spacer at the end of the track." help="Width of the spacer." /> - + diff -r 485ccb7874ad -r b10b77f55859 macros.xml.orig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml.orig Wed Mar 07 02:26:18 2018 -0500 @@ -0,0 +1,585 @@ + + \${GALAXY_SLOTS:-4} +<<<<<<< HEAD + 2.0 + + + #if $use_range.select_use_range == "yes_use_range": + --range $range_min:$range_max + #end if + + +======= + 2.1alpha1 +>>>>>>> joachimwolff-master + + + hicexplorer + + + @BINARY@ --version + + + + + 10.5281/zenodo.1133705 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #set $matrices = [] + #set $mlabels = [] + #for $counter, $i in enumerate($input_files): + ln -s $i.matrix #echo str($counter)+'_matrix'#; + #silent $matrices.append( '%s_matrix' % $counter ) + + #if str($i.mlabel.value) != "": + #set $mlabels += ['"%s"' % ($i.mlabel.value)] + #else + #set $mlabels += ['"%s"' % ($i.matrix.name)] + #end if + #end for + #set $mlabels = ' '.join($mlabels) + #set $matrices = ' '.join($matrices) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + #if $advancedOpt.used_multiple_regions.used_multiple_regions_options == 'no': + #if $advancedOpt.used_multiple_regions.clustering.clustering_options == 'kmeans': + #if int($advancedOpt.used_multiple_regions.clustering.k_kmeans) > 0: + --kmeans $advancedOpt.used_multiple_regions.clustering.k_kmeans + #end if + #end if + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +.. class:: infomark + +For more information on the tools, please visit our `help site`_. + +If you would like to give us feedback or you run into any trouble, please send an email to deeptools@googlegroups.com + +This tool is developed by the `Bioinformatics and Deep-Sequencing Unit`_ at the `Max Planck Institute for Immunobiology and Epigenetics`_. + +.. _Bioinformatics and Deep-Sequencing Unit: http://www3.ie-freiburg.mpg.de/facilities/research-facilities/bioinformatics-and-deep-sequencing-unit/ +.. _Max Planck Institute for Immunobiology and Epigenetics: http://www3.ie-freiburg.mpg.de +.. _help site: https://hicexplorer.readthedocs.org + + + + + + + + + + + + + + + + + + + + + + + + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + #set files=[] + #set labels=[] + #for $i in $input_files: + #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + #silent os.system("ln -s %s %s.bam" % (str($i.bamfile), $temp_input_path)) + #silent os.system("ln -s %s %s.bam.bai" % (str($i.bamfile.metadata.bam_index), $temp_input_path)) + #silent $files.append('%s.bam' % $temp_input_path) + + ##set $files += [str($i.bamfile)] + #if str($i.label.value) != "": + #set $labels += ["\"%s\"" % ($i.label.value)] + #else + #set $labels += ["\"%s\"" % ($i.bamfile.name)] + #end if + #end for + + + + #import tempfile + #set $temp_dir = os.path.abspath(tempfile.mkdtemp()) + #set files=[] + #set labels=[] + #for $i in $input_files: + #set $temp_input_handle = tempfile.NamedTemporaryFile( dir=$temp_dir ) + #set $temp_input_path = $temp_input_handle.name + #silent $temp_input_handle.close() + #silent os.system("ln -s %s %s.bw" % (str($i.bigwigfile), $temp_input_path)) + #silent $files.append('%s.bw' % $temp_input_path) + + ##set $files += [str($i.bigwigfile)] + #if str($i.label.value) != "": + #set $labels += ["\"%s\"" % ($i.label.value)] + #else + #set $labels += ["\"%s\"" % ($i.bigwigfile.name)] + #end if + #end for + + + + + + + + + + + + + + + + + + + + + + + + #if $source.ref_source=="history": + --genome $source.input1 + #else: + --genome "${source.input1_2bit.fields.path}" + #end if + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveMatrix'] is True + )) + + + + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveData'] is True + )) + + + + + (( + output['showOutputSettings'] == 'yes' and + output['saveSortedRegions'] is True + )) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r 485ccb7874ad -r b10b77f55859 test-data/Li_chrX30-35_cool.png Binary file test-data/Li_chrX30-35_cool.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/compare_matrices_log2ratio.h5 Binary file test-data/compare_matrices_log2ratio.h5 has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/compare_matrices_pearson_ratio.cool Binary file test-data/compare_matrices_pearson_ratio.cool has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/covariance_small_50kb.cool Binary file test-data/covariance_small_50kb.cool has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/covariance_small_50kb.h5 Binary file test-data/covariance_small_50kb.h5 has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/diagnostic_plot.png Binary file test-data/diagnostic_plot.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicAggregateContacts_results1.png Binary file test-data/hicAggregateContacts_results1.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicCorrectMatrix_result1.npz.h5 Binary file test-data/hicCorrectMatrix_result1.npz.h5 has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicCorrelate_heatmap_result1.png Binary file test-data/hicCorrelate_heatmap_result1.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicCorrelate_scatter_result1.png Binary file test-data/hicCorrelate_scatter_result1.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicMergeMatrixBins_result1.npz.h5 Binary file test-data/hicMergeMatrixBins_result1.npz.h5 has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicPlotDistVsCounts_result1.png Binary file test-data/hicPlotDistVsCounts_result1.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicPlotDistVsCounts_result2.png Binary file test-data/hicPlotDistVsCounts_result2.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/hicSumMatrices_result1.npz.h5 Binary file test-data/hicSumMatrices_result1.npz.h5 has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/li_viewpoint_32-33Mb.png Binary file test-data/li_viewpoint_32-33Mb.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/li_viewpoint_32Mb.png Binary file test-data/li_viewpoint_32Mb.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/master_TADs_plot.png Binary file test-data/master_TADs_plot.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/master_matrix_plot.png Binary file test-data/master_matrix_plot.png has changed diff -r 485ccb7874ad -r b10b77f55859 test-data/multiFDR_boundaries.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.bed Wed Mar 07 02:26:18 2018 -0500 @@ -0,0 +1,2 @@ +chr2L 22922500 22927500 B04585 -0.068256362891 . +chrX 87500 92500 B19358 -0.072020401017 . diff -r 485ccb7874ad -r b10b77f55859 test-data/multiFDR_boundaries.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_boundaries.gff Wed Mar 07 02:26:18 2018 -0500 @@ -0,0 +1,2 @@ +chr2L HiCExplorer boundary 22922500 22927500 -0.068256362891 . . ID=B04585;delta=0.021954846720;pvalue=0.000033964776;tad_sep=-0.068256362891 +chrX HiCExplorer boundary 87500 92500 -0.072020401017 . . ID=B19358;delta=0.019799980104;pvalue=0.000055223433;tad_sep=-0.072020401017 diff -r 485ccb7874ad -r b10b77f55859 test-data/multiFDR_domains.bed diff -r 485ccb7874ad -r b10b77f55859 test-data/multiFDR_score.bedgraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/multiFDR_score.bedgraph Wed Mar 07 02:26:18 2018 -0500 @@ -0,0 +1,23814 @@ +chr2L 2500 7500 -0.164488846397 +chr2L 7500 12500 0.004155516280 +chr2L 12500 17500 0.260509497302 +chr2L 17500 22500 0.126728724578 +chr2L 22500 27500 0.107536542495 +chr2L 27500 32500 0.067996441287 +chr2L 32500 37500 0.180067325085 +chr2L 37500 42500 0.188704045555 +chr2L 42500 47500 0.123071283383 +chr2L 47500 52500 0.090946822420 +chr2L 52500 57500 0.050290136708 +chr2L 57500 62500 0.043738171585 +chr2L 62500 67500 0.036458137676 +chr2L 67500 72500 -0.008311665224 +chr2L 72500 77500 -0.025506335364 +chr2L 77500 82500 -0.028782499450 +chr2L 82500 87500 -0.008859983289 +chr2L 87500 92500 0.012581289189 +chr2L 92500 97500 -0.026656341295 +chr2L 97500 102500 -0.064470557052 +chr2L 102500 107500 -0.022699733707 +chr2L 107500 112500 -0.026264267296 +chr2L 112500 117500 -0.009926677809 +chr2L 117500 122500 -0.006876513913 +chr2L 122500 127500 0.016147318959 +chr2L 127500 132500 0.022378914981 +chr2L 132500 137500 0.070952047599 +chr2L 137500 142500 0.071053469305 +chr2L 142500 147500 0.068034199638 +chr2L 147500 152500 0.067090397637 +chr2L 152500 157500 0.057311311696 +chr2L 157500 162500 0.067610279560 +chr2L 162500 167500 0.029002777185 +chr2L 167500 172500 0.029002777185 +chr2L 172500 177500 0.008980247068 +chr2L 177500 182500 0.016907224460 +chr2L 182500 187500 -0.000150569937 +chr2L 187500 192500 0.010495785312 +chr2L 192500 197500 -0.048163268016 +chr2L 197500 202500 -0.039867994837 +chr2L 202500 207500 -0.046910414090 +chr2L 207500 212500 -0.055696730183 +chr2L 212500 217500 -0.036501614110 +chr2L 217500 222500 -0.036501614110 +chr2L 222500 227500 -0.023335648652 +chr2L 227500 232500 -0.023335648652 +chr2L 232500 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-0.056245728652 +chr2L 507500 512500 -0.064541001831 +chr2L 512500 517500 -0.071946857401 +chr2L 517500 522500 -0.071946857401 +chr2L 522500 527500 -0.071946857401 +chr2L 527500 532500 -0.076979302876 +chr2L 532500 537500 -0.076979302876 +chr2L 537500 542500 -0.076979302876 +chr2L 542500 547500 -0.120135452320 +chr2L 547500 552500 -0.107649833515 +chr2L 552500 557500 -0.087399804832 +chr2L 557500 562500 -0.099885423637 +chr2L 562500 567500 -0.099885423637 +chr2L 567500 572500 -0.099885423637 +chr2L 572500 577500 -0.099885423637 +chr2L 577500 582500 -0.099885423637 +chr2L 582500 587500 -0.084057834311 +chr2L 587500 592500 -0.084057834311 +chr2L 592500 597500 -0.065926294209 +chr2L 597500 602500 -0.076626770847 +chr2L 602500 607500 -0.063204938090 +chr2L 607500 612500 -0.066951827756 +chr2L 612500 617500 -0.066951827756 +chr2L 617500 622500 -0.095049772135 +chr2L 622500 627500 -0.086559234121 +chr2L 627500 632500 -0.104690774223 +chr2L 632500 637500 -0.104690774223 +chr2L 637500 642500 -0.104690774223 +chr2L 642500 647500 -0.104690774223 +chr2L 647500 652500 -0.053713171413 +chr2L 652500 657500 -0.032383933202 +chr2L 657500 662500 -0.013390883314 +chr2L 662500 667500 -0.023624746219 +chr2L 667500 672500 -0.015426022630 +chr2L 672500 677500 -0.013822637003 +chr2L 677500 682500 -0.013822637003 +chr2L 682500 687500 -0.028847855386 +chr2L 687500 692500 0.017132537265 +chr2L 692500 697500 0.017132537265 +chr2L 697500 702500 0.045710448555 +chr2L 702500 707500 0.027583820124 +chr2L 707500 712500 -0.028547755658 +chr2L 712500 717500 -0.000317643464 +chr2L 717500 722500 -0.014643992043 +chr2L 722500 727500 -0.014643992043 +chr2L 727500 732500 -0.017732383711 +chr2L 732500 737500 0.001546317552 +chr2L 737500 742500 -0.014947679217 +chr2L 742500 747500 -0.007136697412 +chr2L 747500 752500 -0.023340488177 +chr2L 752500 757500 -0.003090459494 +chr2L 757500 762500 -0.002431239390 +chr2L 762500 767500 0.019169021058 +chr2L 767500 772500 0.056276552730 +chr2L 772500 777500 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